scholarly journals Exploring the conformational transition between the fully folded and locally unfolded substates of Escherichia coli thiol peroxidase

2020 ◽  
Vol 22 (17) ◽  
pp. 9518-9533
Author(s):  
Diego S. Vazquez ◽  
Ari Zeida ◽  
William A. Agudelo ◽  
Mónica R. Montes ◽  
Gerardo Ferrer-Sueta ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Transition ◽  
Accelerated Molecular Dynamics ◽  
Thiol Peroxidase ◽  
Dynamics Simulations ◽  
Conformational Substate

Temporal acquisition of the fully folded conformational substate of the Escherichia coli thiol peroxidase by accelerated molecular dynamics simulations.

UNDERSTANDING DIFFERENT LCST LEVELS OF POLY(N-ALKYLACRYLAMIDE)S BY MOLECULAR DYNAMICS SIMULATIONS AND QUANTUM MECHANICS CALCULATIONS

2011 ◽  
Vol 10 (03) ◽  
pp. 359-370 ◽  
Author(s):  
JUAN PANG ◽  
HU YANG ◽  
JING MA ◽  
RONGSHI CHENG
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Aqueous Solutions ◽  
Molecular Dynamics Simulations ◽  
Steric Effect ◽  
Conformational Transition ◽  
Methyl Group ◽  
Branched Chain ◽  
Dynamics Simulations ◽  
Different Levels

Poly(N-alkylacrylamide) is a group of thermo-sensitive polymers that include poly (N-isopropylacrylamide), poly(N-n-propylacrylamide), poly(N-isopropylmethacryl-amide), and so on. The polymers exhibit different levels of lower critical solution temperatures (LCST) in aqueous solutions. In this article, their monomers and oligomers with 10 repeating units are selected, respectively, to demonstrate the cause of different LCST levels of the polymers in aqueous solutions using molecular dynamics simulations and quantum mechanics calculations. The monomers have functional groups of different steric volume that greatly affect the conformational transition of chains and LCST levels of the polymers. A branched chain of N-propyl group in N-isopropylacrylamide and an additional methyl group at α-carbon in N-isopropylmethacrylamide both increase the steric effect, making it more difficult for monomers to draw closer and resulting in higher LCST levels of the polymers. In addition, the simulated results from their corresponding oligomers exhibit the similar trend to those from the monomers.

scholarly journals Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations

2011 ◽  
Vol 8 (1) ◽  
pp. 17-23 ◽  
Author(s):  
William Sinko ◽  
César Augusto F. de Oliveira ◽  
Levi C. T. Pierce ◽  
J. Andrew McCammon
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
High Energy ◽  
Energy Barriers ◽  
Accelerated Molecular Dynamics ◽  
New Equation ◽  
Dynamics Simulations

scholarly journals Bayesian Refinement of Accelerated Molecular Dynamics Simulations for Interpreting SAXS Experiments

2017 ◽  
Vol 112 (3) ◽  
pp. 580a
Author(s):  
Samuel Bowerman ◽  
Amy Rice ◽  
Jeff Wereszczynski
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Accelerated Molecular Dynamics ◽  
Dynamics Simulations

Accelerated molecular dynamics simulations of interstitial clusters in pure and Al-doped MgO

2006 ◽  
Vol 250 (1-2) ◽  
pp. 12-16 ◽  
Author(s):  
B.P. Uberuaga ◽  
R. Smith ◽  
A.R. Cleave ◽  
R.W. Grimes ◽  
A.F. Voter ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Accelerated Molecular Dynamics ◽  
Dynamics Simulations
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